[English] 日本語
Yorodumi
- PDB-4l18: Crystal structure of Runx1 and Ets1 bound to TCR alpha promoter (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l18
TitleCrystal structure of Runx1 and Ets1 bound to TCR alpha promoter (crystal form 3)
Components
  • 5'-D(*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3'
  • 5'-D(*GP*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3'
  • Protein C-ets-1
  • Runt-related transcription factor 1
KeywordsTRANSCRIPTION/DNA / RUNT domain / ETS domain / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


regulation of hair follicle cell proliferation / Organic cation transport / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / Regulation of RUNX1 Expression and Activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of granulocyte differentiation / core-binding factor complex ...regulation of hair follicle cell proliferation / Organic cation transport / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / Regulation of RUNX1 Expression and Activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of granulocyte differentiation / core-binding factor complex / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of CD8-positive, alpha-beta T cell differentiation / positive regulation of cell maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / PML body organization / neuron fate commitment / Estrogen-dependent gene expression / myeloid progenitor cell differentiation / definitive hemopoiesis / regulation of T cell anergy / positive regulation of leukocyte adhesion to vascular endothelial cell / embryonic hemopoiesis / hair follicle morphogenesis / behavioral response to pain / hemopoiesis / basement membrane / negative regulation of cell cycle / positive regulation of blood vessel endothelial cell migration / regulation of signal transduction / regulation of angiogenesis / neuron development / response to retinoic acid / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell migration / positive regulation of interleukin-2 production / positive regulation of erythrocyte differentiation / liver development / central nervous system development / transcription corepressor binding / skeletal system development / cell motility / Oncogene Induced Senescence / positive regulation of miRNA transcription / positive regulation of type II interferon production / positive regulation of inflammatory response / neuron differentiation / positive regulation of angiogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / gene expression / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / transcription by RNA polymerase II / nucleic acid binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / response to antibiotic / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / Protein C-ets-1, pointed domain / Transforming protein C-ets ...Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Immunoglobulin-like - #720 / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Sterile alpha motif/pointed domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein C-ets-1 / Runt-related transcription factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTahirov, T.H.
CitationJournal: Leukemia / Year: 2014
Title: Structural basis of Ets1 activation by Runx1.
Authors: Shrivastava, T. / Mino, K. / Babayeva, N.D. / Baranovskaya, O.I. / Rizzino, A. / Tahirov, T.H.
History
DepositionJun 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Runt-related transcription factor 1
B: Protein C-ets-1
C: 5'-D(*GP*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3'
D: 5'-D(*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3'
E: Runt-related transcription factor 1
F: Protein C-ets-1
G: 5'-D(*GP*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3'
H: 5'-D(*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1169
Polymers91,0248
Non-polymers921
Water2,576143
1
A: Runt-related transcription factor 1
B: Protein C-ets-1
C: 5'-D(*GP*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3'
D: 5'-D(*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6045
Polymers45,5124
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-37 kcal/mol
Surface area17370 Å2
MethodPISA
2
E: Runt-related transcription factor 1
F: Protein C-ets-1
G: 5'-D(*GP*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3'
H: 5'-D(*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3'


Theoretical massNumber of molelcules
Total (without water)45,5124
Polymers45,5124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-33 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.153, 100.032, 72.064
Angle α, β, γ (deg.)90.00, 110.23, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules AEBF

#1: Protein Runt-related transcription factor 1 / Runx1 / Acute myeloid leukemia 1 protein / Core-binding factor subunit alpha-2 / CBF-alpha-2 / ...Runx1 / Acute myeloid leukemia 1 protein / Core-binding factor subunit alpha-2 / CBF-alpha-2 / Oncogene AML-1 / Polyomavirus enhancer-binding protein 2 alpha B subunit / PEA2-alpha B / PEBP2-alpha B / SL3-3 enhancer factor 1 alpha B subunit / SL3/AKV core-binding factor alpha B subunit


Mass: 18741.350 Da / Num. of mol.: 2 / Fragment: UNP residues 48-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Runx1, Aml1, Cbfa2, Pebp2ab / Production host: Escherichia coli (E. coli) / References: UniProt: Q03347
#2: Protein Protein C-ets-1 / Ets1 / p54


Mass: 16973.369 Da / Num. of mol.: 2 / Fragment: UNP residues 296-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETS1, EWSR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14921

-
DNA chain , 2 types, 4 molecules CGDH

#3: DNA chain 5'-D(*GP*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3'


Mass: 4843.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: TCR alpha DNA strand 1 / Source: (synth.) Homo sapiens (human)
#4: DNA chain 5'-D(*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3'


Mass: 4954.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: TCR alpha DNA strand 2 / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 2 types, 144 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2.5% w/v PEG4000, 5 mM magnesium chloride hexahydrate, 25 mM MES, pH 5.6, 5% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 35376 / % possible obs: 92.4 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3.2 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 26.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1128 / % possible all: 60.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.64 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1680438.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1665 4.9 %RANDOM
Rwork0.231 ---
obs0.231 33721 87.5 %-
all-0 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.7266 Å2 / ksol: 0.352857 e/Å3
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20.92 Å2
2--1 Å20 Å2
3---0.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.44 Å
Luzzati d res low-20 Å
Luzzati sigma a0.67 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 1300 6 143 5431
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.491.5
X-RAY DIFFRACTIONc_mcangle_it5.322
X-RAY DIFFRACTIONc_scbond_it5.182
X-RAY DIFFRACTIONc_scangle_it6.842.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.445 154 4.6 %
Rwork0.487 3167 -
obs--50.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4gol.pargol.top

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more